A young boy named AGITO enters a forbidden sanctuary where a glowing machine preserves the young girl Toola, who has a mission entrusted by her from the past. 300 years into the future, the Earth's environment has been ruined by the human race, and in between the 300 years, past humans were forced into deep sleep. The Earth has now reached a point where if humans were to survive, must find ways to break out of a subsidiary existence in "The Forest", and defend themselves against the city Laguna, which has become a military power.